R Notebook
Running chromVAR
Add in the other ATAC of differentiated things and run chromVAR to see the maintenance of Oct4:Sox2 in NC compared to differentiated cells.
library(GenomicRanges)
library(BiocParallel)
library(tibble)
library(dplyr)
library(GenomicFeatures)
library(chromVAR)
library(DiffBind)
library(JASPAR2020)
library(TFBSTools)
library(motifmatchr)
library(BSgenome.Hsapiens.UCSC.hg38)
library(ggplot2)
library(cowplot)
register(BPPARAM = MulticoreParam(workers = 62, progressbar = TRUE))Creating chromVAR dev’s and plotting PCA.
I want to re-run this with resized 400bp peaks and see how muhc of a difference it makes.
#All_dba <- dba(sampleSheet="ESC_SampleSheet_Master.csv")
All_dba <- dba(sampleSheet="ESC_SampleSheet_CombinedPeaks_NC_Myo.csv")
Removed white space from /data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_ES_D0_1_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_ES_D0_2_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_Myo_D14_1_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_Myo_D14_2_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_NC_D3_1_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_NC_D3_2_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_NC_D5_1_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_NC_D5_2_toGRCh38_sorted_nodups.bam in column bamReads (rows 1,2,3,4,5,6,7,8)Removed white space from /home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed in column Peaks (rows 1,2,3,4,5,6,7,8)#All_dba <- dba(sampleSheet="ESC_SampleSheet_Master.csv")
All_dba <- dba(sampleSheet="ESC_SampleSheet_CombinedPeaks_NC_Myo.csv")Removed white space from /data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_ES_D0_1_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_ES_D0_2_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_Myo_D14_1_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_Myo_D14_2_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_NC_D3_1_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_NC_D3_2_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_NC_D5_1_toGRCh38_sorted_nodups.bam,/data/Austin/workdir/NC_Timecourse_Data/Human_ESC_ATAC/BAM/ATAC_NC_D5_2_toGRCh38_sorted_nodups.bam in column bamReads (rows 1,2,3,4,5,6,7,8)Removed white space from /home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed,/home/ash274/local_git/NC_Timecourse/ATAC-Seq/Human_ESC_iNC/400bp_centered_all_peaks.bed in column Peaks (rows 1,2,3,4,5,6,7,8)All_dba <- dba.count(All_dba)
summarized_experiment2 <- dba(All_dba, bSummarizedExperiment = T)
summarized_experiment2@assays@data$scores <- summarized_experiment2@assays@data$Reads
names(summarized_experiment2@assays) <- c("scores", "RPKM", "counts","cRPKM","cReads")
summarized_experiment2 <- addGCBias(summarized_experiment2, genome = BSgenome.Hsapiens.UCSC.hg38)
head(rowData(summarized_experiment2))DataFrame with 6 rows and 1 column
bias
<numeric>
1 0.544378698224852
2 0.618453865336658
3 0.508728179551122
4 0.605985037406484
5 0.744285714285714
6 0.489841986455982opts <- list()
opts["tax_group"] <- "vertebrates"
opts["collection"] <- "CORE"
motifs <- getMatrixSet(JASPAR2020, opts = opts)
motif_ix <- matchMotifs(motifs, summarized_experiment2, genome = BSgenome.Hsapiens.UCSC.hg38)
dev <- computeDeviations(summarized_experiment2, motif_ix)
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|==========================================================================================================| 100%dev@NAMES <- paste0(dev@NAMES,"_",TFBSTools::name(motifs))
variability <- computeVariability(dev)
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|==========================================================================================================| 100%plotVariability(variability, n = 5)
tsne_dev <- deviationsTsne(dev, shiny = T) #1.8 var cutoff
g <- plotDeviationsTsne(dev, tsne = tsne_dev, sample_column = "Tissue", shiny = F)
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